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Gentoo's Bugzilla – Attachment 245527 Details for
Bug 335447
sci-biology/mummer does not respect LDFLAGS
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Build log
mummer-3.22:20100831-165931.log (text/plain), 13.47 KB, created by
Diego Elio Pettenò (RETIRED)
on 2010-08-31 19:31:32 UTC
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Description:
Build log
Filename:
MIME Type:
Creator:
Diego Elio Pettenò (RETIRED)
Created:
2010-08-31 19:31:32 UTC
Size:
13.47 KB
patch
obsolete
> * CPV: sci-biology/mummer-3.22 > * REPO: gentoo > * USE: elibc_glibc kernel_linux test userland_GNU x86 >>>> Unpacking source... >>>> Unpacking MUMmer3.22.tar.gz to /var/tmp/portage/sci-biology/mummer-3.22/work >>>> Source unpacked in /var/tmp/portage/sci-biology/mummer-3.22/work >>>> Preparing source in /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22 ... >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22 ... >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22 ... >make -j14 >cd /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/src/kurtz; make mummer >cd /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/src/tigr; make all >cd /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/scripts; make all >make[1]: Entering directory `/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/src/kurtz' >cd libbasedir; make libbase.a >make[1]: Entering directory `/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/src/tigr' >/usr/bin/g++ -O3 tigrinc.cc -c -o tigrinc.o >make[2]: Entering directory `/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/src/kurtz/libbasedir' >/usr/bin/gcc -O3 -c -o cleanMUMcand.o cleanMUMcand.c >/usr/bin/g++ -O3 delta.cc -c -o delta.o >make[1]: Entering directory `/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/scripts' >/bin/sed -e 's?__CSH_PATH?/bin/csh?g' \ > -e 's?__BIN_DIR?/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22?g' \ > -e 's?__SCRIPT_DIR?/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/scripts?g' \ > exact-tandems.csh > /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/exact-tandems >/bin/sed -e 's?__PERL_PATH?/usr/bin/perl?g' \ > -e 's?__SCRIPT_DIR?/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/scripts?g' \ > mapview.pl > /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/mapview >/usr/bin/g++ -O3 sw_align.cc -c -o sw_align.o >/usr/bin/g++ -O3 translate.cc -c -o translate.o >/bin/sed -e 's?__PERL_PATH?/usr/bin/perl?g' \ > -e 's?__SCRIPT_DIR?/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/scripts?g' \ > -e 's?__BIN_DIR?/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22?g' \ > mummerplot.pl > /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/mummerplot >/bin/sed -e 's?__PERL_PATH?/usr/bin/perl?g' \ > -e 's?__SCRIPT_DIR?/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/scripts?g' \ > -e 's?__AUX_BIN_DIR?/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/aux_bin?g' \ > -e 's?__BIN_DIR?/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22?g' \ > nucmer.pl > /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/nucmer >/bin/sed -e 's?__PERL_PATH?/usr/bin/perl?g' \ > -e 's?__SCRIPT_DIR?/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/scripts?g' \ > -e 's?__AUX_BIN_DIR?/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/aux_bin?g' \ > -e 's?__BIN_DIR?/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22?g' \ > promer.pl > /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/promer >/bin/sed -e 's?__CSH_PATH?/bin/csh?g' \ > -e 's?__BIN_DIR?/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22?g' \ > run-mummer1.csh > /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/run-mummer1 >chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/exact-tandems >/usr/bin/gcc -O3 -c -o clock.o clock.c >/usr/bin/gcc -O3 -c -o mapfile.o mapfile.c >/bin/sed -e 's?__CSH_PATH?/bin/csh?g' \ > -e 's?__BIN_DIR?/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22?g' \ > run-mummer3.csh > /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/run-mummer3 >chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/mapview >chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/mummerplot >chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/nucmer >chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/promer >chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/run-mummer1 >/usr/bin/gcc -O3 -c -o multiseq.o multiseq.c >/bin/sed -e 's?__PERL_PATH?/usr/bin/perl?g' \ > nucmer2xfig.pl > /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/nucmer2xfig >/usr/bin/gcc -O3 -c -o procopt.o procopt.c >/bin/sed -e 's?__PERL_PATH?/usr/bin/perl?g' \ > -e 's?__SCRIPT_DIR?/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/scripts?g' \ > -e 's?__BIN_DIR?/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22?g' \ > dnadiff.pl > /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/dnadiff >chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/run-mummer3 >/usr/bin/gcc -O3 -c -o safescpy.o safescpy.c >/usr/bin/gcc -O3 -c -o seterror.o seterror.c >/usr/bin/gcc -O3 -c -o space.o space.c >chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/dnadiff >chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/nucmer2xfig >make[1]: Leaving directory `/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/scripts' >tigrinc.cc: In function âint Read_String(FILE*, char*&, long int&, char*, int)â: >tigrinc.cc:335:30: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â, declared with attribute warn_unused_result >ar sruv libbase.a cleanMUMcand.o clock.o mapfile.o multiseq.o procopt.o safescpy.o seterror.o space.o >ar: creating libbase.a >a - cleanMUMcand.o >a - clock.o >a - mapfile.o >a - multiseq.o >a - procopt.o >a - safescpy.o >a - seterror.o >a - space.o >make[2]: Leaving directory `/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/src/kurtz/libbasedir' >cd streesrc; make libstree.a >make[2]: Entering directory `/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/src/kurtz/streesrc' >/usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE -c -o construct.o construct.c >/usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE -c -o access.o access.c >/usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE -c -o scanpref.o scanpref.c >/usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE -c -o linkloc.o linkloc.c >/usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE -c -o depthtab.o depthtab.c >/usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE -c -o ex2leav.o ex2leav.c >/usr/bin/g++ -O3 annotate.cc tigrinc.o -o /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/annotate; chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/annotate >/usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE -c -o dfs.o dfs.c >/usr/bin/g++ -O3 combineMUMs.cc tigrinc.o -o /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/combineMUMs; chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/combineMUMs >/usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE -c -o overmax.o overmax.c >/usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE -c -o oversucc.o oversucc.c >/usr/bin/g++ -O3 gaps.cc tigrinc.o -o /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/gaps; chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/gaps >/usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE -c -o addleafcount.o addleafcount.c >/usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE -c -o iterator.o iterator.c >/usr/bin/g++ -O3 mgaps.cc tigrinc.o -o /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/mgaps; chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/mgaps >/usr/bin/g++ -O3 prenuc.cc tigrinc.o -o /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/aux_bin/prenuc; chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/aux_bin/prenuc >/usr/bin/g++ -O3 prepro.cc tigrinc.o translate.o -o /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/aux_bin/prepro; chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/aux_bin/prepro >combineMUMs.cc:109:27: warning: deprecated conversion from string constant to âchar*â >combineMUMs.cc:135:24: warning: deprecated conversion from string constant to âchar*â >combineMUMs.cc:145:22: warning: deprecated conversion from string constant to âchar*â >combineMUMs.cc: In function âint Read_String(FILE*, char**, long int*, char*)â: >combineMUMs.cc:1481:30: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â, declared with attribute warn_unused_result >/usr/bin/g++ -O3 repeat-match.cc tigrinc.o -o /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/repeat-match; chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/repeat-match >mgaps.cc: In function âint Process_Cluster(Match_t*, int, char*)â: >mgaps.cc:533:20: warning: deprecated conversion from string constant to âchar*â >mgaps.cc: In function âvoid Process_Matches(Match_t*, int, char*)â: >mgaps.cc:620:19: warning: deprecated conversion from string constant to âchar*â >/usr/bin/g++ -O3 postnuc.cc tigrinc.o sw_align.o -o /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/aux_bin/postnuc; chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/aux_bin/postnuc >/usr/bin/g++ -O3 postpro.cc tigrinc.o sw_align.o translate.o -o /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/aux_bin/postpro; chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/aux_bin/postpro >ar sruv libstree.a construct.o access.o scanpref.o linkloc.o depthtab.o ex2leav.o dfs.o overmax.o oversucc.o addleafcount.o iterator.o >ar: creating libstree.a >a - construct.o >a - access.o >a - scanpref.o >a - linkloc.o >a - depthtab.o >a - ex2leav.o >a - dfs.o >a - overmax.o >a - oversucc.o >a - addleafcount.o >a - iterator.o >make[2]: Leaving directory `/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/src/kurtz/streesrc' >cd mm3src; make mummer >make[2]: Entering directory `/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/src/kurtz/mm3src' >/usr/bin/gcc -O3 -I../libbasedir -I../streesrc -c -o maxmat3.o maxmat3.c >/usr/bin/gcc -O3 -I../libbasedir -I../streesrc -c -o maxmatopt.o maxmatopt.c >/usr/bin/gcc -O3 -I../libbasedir -I../streesrc -c -o maxmatinp.o maxmatinp.c >/usr/bin/gcc -O3 -I../libbasedir -I../streesrc -c -o findmumcand.o findmumcand.c >/usr/bin/gcc -O3 -I../libbasedir -I../streesrc -c -o findmaxmat.o findmaxmat.c >/usr/bin/gcc -O3 -I../libbasedir -I../streesrc -c -o procmaxmat.o procmaxmat.c >/usr/bin/gcc -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu maxmat3.o maxmatopt.o maxmatinp.o findmumcand.o findmaxmat.o procmaxmat.o ../streesrc/libstree.a ../libbasedir/libbase.a \ >-o /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/mummer; chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/mummer >make[2]: Leaving directory `/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/src/kurtz/mm3src' >make[1]: Leaving directory `/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/src/kurtz' >/usr/bin/g++ -O3 delta-filter.cc tigrinc.o delta.o -o /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/delta-filter; chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/delta-filter >/usr/bin/g++ -O3 show-aligns.cc tigrinc.o translate.o delta.o -o /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/show-aligns; chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/show-aligns >/usr/bin/g++ -O3 show-coords.cc tigrinc.o delta.o -o /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/show-coords; chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/show-coords >/usr/bin/g++ -O3 show-tiling.cc tigrinc.o delta.o -o /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/show-tiling; chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/show-tiling >/usr/bin/g++ -O3 show-snps.cc tigrinc.o translate.o delta.o -o /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/show-snps; chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/show-snps >/usr/bin/g++ -O3 show-diff.cc tigrinc.o delta.o -o /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/show-diff; chmod 755 /var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/show-diff >show-coords.cc: In function âvoid printBtab(std::vector<AlignStats>)â: >show-coords.cc:799:12: warning: deprecated conversion from string constant to âchar*â >show-coords.cc:801:12: warning: deprecated conversion from string constant to âchar*â >show-coords.cc:803:12: warning: deprecated conversion from string constant to âchar*â >make[1]: Leaving directory `/var/tmp/portage/sci-biology/mummer-3.22/work/MUMmer3.22/src/tigr' >>>> Source compiled. >>>> Test phase [check]: sci-biology/mummer-3.22 >make -j14 -j1 check >check complete > >>>> Install mummer-3.22 into /var/tmp/portage/sci-biology/mummer-3.22/image/ category sci-biology >>>> Completed installing mummer-3.22 into /var/tmp/portage/sci-biology/mummer-3.22/image/ > >strip: i686-pc-linux-gnu-strip --strip-unneeded -R .comment > usr/bin/repeat-match > usr/bin/gaps > usr/bin/show-tiling > usr/bin/show-coords > usr/bin/prenuc > usr/bin/combineMUMs > usr/bin/mgaps > usr/bin/show-snps > usr/bin/mummer > usr/bin/mummer-annotate > usr/bin/show-aligns > usr/bin/show-diff > usr/bin/postpro > usr/bin/postnuc > usr/bin/delta-filter > usr/bin/prepro > > * QA Notice: Files built without respecting LDFLAGS have been detected > * Please include the following list of files in your report: > * /usr/bin/repeat-match > * /usr/bin/gaps > * /usr/bin/show-tiling > * /usr/bin/show-coords > * /usr/bin/prenuc > * /usr/bin/combineMUMs > * /usr/bin/mgaps > * /usr/bin/show-snps > * /usr/bin/mummer-annotate > * /usr/bin/show-aligns > * /usr/bin/show-diff > * /usr/bin/postpro > * /usr/bin/postnuc > * /usr/bin/delta-filter > * /usr/bin/prepro > > * Gentoo contact information ... >herds: > sci-biology >maintainers: > weaver@gentoo.org >
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: 245527